Spatial Omics
Bring omics data into the spatial dimension and reconstruct molecular expression and tissue architecture in situ.
10x Visium HD
10x Visium HD is a next-generation high-throughput spatial-omics technology from 10x Genomics that dramatically improves spatial resolution over standard Visium. Using a high-density capture array, it acquires whole-transcriptome profiles with near-single-cell resolution while preserving tissue morphology, capturing close-range cell interactions and microenvironment zoning. Breaking the 'spot-level' limitation, it increases capture density several-fold and remains compatible with fresh-frozen and FFPE tissue. Ideal for high-resolution TME, neural circuits, and developmental tracking—identifying niches and spatial co-localization to reveal complex tissue regulation.
Principle Introduction
Visium HD retains 'spatial barcode labeling–in-situ capture–sequencing' but uses an ultra-high-density array with much smaller spot pitch for near-single-cell localization. Permeabilization releases mRNA bound to neighboring probes with unique barcodes. For FFPE, an optimized RNA-repair system improves recovery. Sequencing reads map back via barcodes; cell-segmentation algorithms generate high-resolution 3-in-1 maps distinguishing mixed-cell expression.
Literature
Published in Nature Genetics, a Visium HD + single-cell multi-omics study built the first ultra-high-resolution spatial transcriptome atlas of adult human prostate across peripheral, transition, and central zones. Visium HD resolved epithelial, stromal, and immune distributions and identified fibroblast subpopulations around glands; high-resolution analysis revealed hormone-regulation gradients and epithelial–immune proximity, providing spatial targets for prostate cancer.
Sample Requirements
5 μm sections, ≥3/sample, charged slides; -80°C, dry ice; freeze within 30 min.
block ≥0.3×0.3×0.2 cm, sections 5 μm, ≥5/sample; block ambient, sections refrigerated; fixation 6–24 h, ≤5 years, necrosis <20%.
include core/boundary/normal; note type, stage, history; FFPE needs pathology grade, fresh frozen within 4 h.
fresh snap-frozen, 5 μm; FFPE fixed strictly.
≥0.2×0.2×0.1 cm, 4°C or frozen; 2–3 sections with location notes.
Deliverables
Raw data
Fastq, spatial barcode stats, QC (GC, duplication), high-res spot signal.
Analysis
ultra-high-resolution expression map, fine cell-type localization, differential genes, niche identification, spatial interaction.
FAQ
Uniform 5 μm sections, optimize permeabilization, scRNA validation, professional algorithms.
Prefer ≤3 years, 6–24 h fixation; optimize dewaxing/RNA repair; avoid high necrosis.
Use HEARTSVG for variable‑gene selection/clustering; register with pathology images; integrate multi‑omics.
